The head kidney, analogous to the mammalian adrenal gland, is an organ unique for teleost fish. It comprises cytokine-producing lymphoid cells from the immune system and endocrine cells secreting cortisol, catecholamines, and thyroid hormones. The intimate organization of the immune system and endocrine system in one single organ makes bidirectional signalling between these possible. In this review we explore putative interactions between the thyroid and immune system in the head kidney. We give a short overview of the thyroid system, and consider the evidence for the presence of thyroid follicles in the head kidney as a normal, healthy trait in fishes. From mammalian studies we gather data on the effects of three important pro-inflammatory cytokines (TNFalpha, IL-1beta, IL-6) on the thyroid system. A general picture that emerges is that pro-inflammatory cytokines inhibit the activity of the thyroid system at different targets. Extrapolating from these studies, we suggest that the interaction of the thyroid system by paracrine actions of cytokines in the head kidney is involved in fine-tuning the availability and redistribution of energy substrates during acclimation processes such as an immune response or stress response.